You could consider using mass balance approach for something that is easy to measure (e.g., water evaporation from emitting soil) and then correlate it with flux of target gases of interest. See this publication for ideas.:
Parker, D.B., N.A. Cole, K.D. Casey, G. Galvin, R. Ormerod, C.S. Paris, E.A. Caraway, M.B. Rhoades. 2009. Wind tunnels vs. flux chambers: Area source emission measurements and the necessity for VOC and odour correction factors. Proceedings 19th International Clean Air and Environment Conference, Perth, Australia, September 6-9, 2009.
This correct, but I also want to know if there a direct method such as titration or something simple to measure CO2, CH4 and N2O from incubated soil samples?
see this article for the soda lime method that Zsolt suggested:
Keith, H. and Wong, S.C., 2006. Measurement of soil CO 2 efflux using soda lime absorption: both quantitative and reliable. Soil Biology and Biochemistry, 38(5), pp.1121-1131.
Soda lime method creates a lot of biases and is not really recommended for any estimates. I suppose, you can use cheap optical sensors (100-500$) for CO2 and methane but it will work only for a strong sources. For N2O it seems impossible up to the moment.
I think, this option is the most cost-effective and reliable for CO2 (sensor is described in paper): http://www.biogeosciences.net/12/3849/2015/bg-12-3849-2015.html
For methane and N2O there are no cheap options for small fluxes.
I think the labour intensive nature of flux surveys is often overstated. I can routinely make 100 - 200 flux measurements per day on my own. However, this does depend on they type of measurement you are doing - spatial or temporal, and the suitability and responsiveness of the equipment you are using. There is a lot of work required to produce an accurate flux meter. Have you looked at the time it takes vs the $ to buy a West Systems Diffuse Flux Meter or a Li-COR equivalent?